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GATB-Pipeline

Docker image for the GATB-pipeline assembler

Sample commands:

You can take example from the following commands to build and run the GATB-pipeline assembler container.

To build the docker image:

docker build -t gatb/gatb-pipeline .

Then define the following 2 directories:

export dir1=...  # where your input data are located on the host machine
                 # (this directory will be mounted inside the container 
                 # as /inputs)

export dir2=...  # where you want to mount the container run directory
                 # on your host machine (for runtime monitoring)

Finally, launch the run:

docker run -it --rm -v $dir1:/inputs -v $dir2:/tmp/gatb-pipeline gatb/gatb-pipeline SRR531199 /inputs /tmp/gatb-pipeline

where SRR531199 is the codename of your experiment (see Procfile).

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rchikhi
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